2CCZ

Crystal structure of E. coli primosomol protein PriB bound to ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Complexed Crystal Structure of Replication Restart Primsome Protein Prib Reveals a Novel Single-Stranded DNA-Binding Mode.

Huang, C.-Y.Hsu, C.-H.Sun, Y.-J.Wu, H.-N.Hsiao, C.-D.

(2006) Nucleic Acids Res 34: 3878

  • DOI: 10.1093/nar/gkl536
  • Primary Citation of Related Structures:  
    2CCZ

  • PubMed Abstract: 
  • PriB is a primosomal protein required for replication restart in Escherichia coli. PriB stimulates PriA helicase activity via interaction with single-stranded DNA (ssDNA), but the molecular details of this interaction remain unclear. Here, we report ...

    PriB is a primosomal protein required for replication restart in Escherichia coli. PriB stimulates PriA helicase activity via interaction with single-stranded DNA (ssDNA), but the molecular details of this interaction remain unclear. Here, we report the crystal structure of PriB complexed with a 15 bases oligonucleotide (dT15) at 2.7 A resolution. PriB shares structural similarity with the E.coli ssDNA-binding protein (EcoSSB). However, the structure of the PriB-dT15 complex reveals that PriB binds ssDNA differently. Results from filter-binding assays show that PriB-ssDNA interaction is salt-sensitive and cooperative. Mutational analysis suggests that the loop L45 plays an important role in ssDNA binding. Based on the crystal structure and biochemical analyses, we propose a cooperative mechanism for the binding of PriB to ssDNA and a model for the assembly of the PriA-PriB-ssDNA complex. This report presents the first structure of a replication restart primosomal protein complexed with DNA, and a novel model that explains the interactions between a dimeric oligonucleotide-binding-fold protein and ssDNA.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRIMOSOMAL REPLICATION PROTEIN NAB123Escherichia coli K-12Mutation(s): 1 
Gene Names: priBb4201JW4159
Find proteins for P07013 (Escherichia coli (strain K12))
Explore P07013 
Go to UniProtKB:  P07013
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3'C15N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.284 
    • R-Value Work: 0.250 
    • R-Value Observed: 0.250 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 45.537α = 90
    b = 51.148β = 90
    c = 99.096γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    AMoREphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2006-09-18
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance